Commit 0ccac08b authored by Kosmas Hench's avatar Kosmas Hench
Browse files

update documentation of figure 1 - 3

parent d7507191

0_data/0_resources/F2.karyo.txt

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START	END	CHROM	GSTART

0	25890264	LG01

0	31702000	LG02

0	23122023	LG03

0	25000711	LG04

0	20912025	LG05

0	24210077	LG06

0	24100755	LG07

0	27000498	LG08

0	27186781	LG09

0	21876389	LG10

0	21320898	LG11

0	25506241	LG12

0	26810734	LG13

0	22338278	LG14

0	21633613	LG15

0	24734982	LG16

0	28429713	LG17

0	19773282	LG18

0	27051319	LG19

0	24942031	LG20

0	20142184	LG21

0	13699534	LG22

0	17761902	LG23

0	14503443	LG24

0_data/0_scripts/F3.functions.R

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get_anno_df_single_line <- function(searchLG,gfffile,

                                    xrange,

                                    genes_of_interest,

                                    genes_of_sec_interest,

                                    anno_rown=3){

  gff_filter <- list(seqid=searchLG)

  data <- as.data.frame(readGFF(gfffile,filter=gff_filter)) %>% mutate(Parent=as.character(Parent))#%>%

  #rowwise() %>% mutate(Parent=ifelse(length(Parent)==0,ID,Parent))

  

  mRNAs <- data %>% filter(type=='mRNA',end>xrange[1],start<xrange[2]) %>% 

    ungroup() %>%  mutate(yl=row_number()%%anno_rown+2) %>% rowwise()%>%

    mutate(checkStart =ifelse(start<xrange[1],-Inf,start),

           checkEnd =ifelse(end>xrange[2],Inf,end),

           ps=ifelse(strand=='-',checkEnd,checkStart),

           pe=ifelse(strand=='-',checkStart,checkEnd),

           labelx=mean(c(sort(c(xrange[1],ps))[2],

                         sort(c(xrange[2],pe))[1])),

           window='bold(Gene)',

           clr=ifelse(Parentgenename %in% genes_of_interest,"y",

                      ifelse(Parentgenename %in% genes_of_sec_interest,"z","x"))) %>% 

    select(-Parent);

  names(mRNAs)[names(mRNAs)=='ID'] <- 'Parent'

  

  exons <- data %>% filter(type=='exon',end>xrange[1],start<xrange[2]) %>% 

    merge(.,mRNAs %>% select(Parent,yl,clr),by='Parent',all.x=T) %>% 

    mutate(ps=ifelse(strand=='-',end,start),

           pe=ifelse(strand=='-',start,end),

           window='bold(Gene)')

  return(list(mRNAs,exons))}

0_data/0_scripts/F3.getDXY.R

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getDXY<- function(searchLG,xr){

    np <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.pue-nig.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-pue')

  nu <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.nig-uni.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-uni')

  pu <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.pue-uni.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='pue-uni')

  

  data_dxy <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(d[XY])')

  

  npB <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.puebel-nigbel.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-pue',group='bel')

  nuB <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.nigbel-unibel.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-uni',group='bel')

  puB <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.puebel-unibel.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='pue-uni',group='bel')

  

  npH <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.puehon-nighon.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-pue',group='hon')

  nuH <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.nighon-unihon.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-uni',group='hon')

  puH <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.puehon-unihon.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='pue-uni',group='hon')

  

  npP <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.pueboc-nigboc.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-pue',group='pan') 

  nuP <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.nigboc-uniboc.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='nig-uni',group='pan')

  puP <- read.csv(gzfile(paste('../../2_output/08_popGen/01_dxy/10kb/',searchLG,'/dxy.pueboc-uniboc.',searchLG,'.10kb-1kb.txt.gz',sep=''))) %>% 

    select(BIN_START,BIN_END,dxy) %>% mutate(run='pue-uni',group='pan')

  

  data_dxy_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pw~d[XY])')

  

  

  return(list(data_dxy_pw=data_dxy_pw,data_dxy=data_dxy))

}
 
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0_data/0_scripts/F3.getFSTs.R

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getFSTS <- function(searchLG,xr,searchsnp,highclr){

  

  np <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/pue-nig.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-pue')

  nu <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/nig-uni.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-uni')

  pu <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/pue-uni.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='pue-uni')

  

  data_fst <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(F[ST])')

  

  npB <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/puebel-nigbel.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-pue',group='bel')

  nuB <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/nigbel-unibel.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-uni',group='bel')

  puB <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/puebel-unibel.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='pue-uni',group='bel')

  

  npH <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/puehon-nighon.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-pue',group='hon')

  nuH <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/nighon-unihon.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-uni',group='hon')

  puH <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/puehon-unihon.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='pue-uni',group='hon')

  

  npP <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/pueboc-nigboc.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-pue',group='pan') 

  nuP <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/nigboc-uniboc.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='nig-uni',group='pan')

  puP <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/pueboc-uniboc.10kb.1kb.windowed.',searchLG,'.fst',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,WEIGHTED_FST) %>% mutate(run='pue-uni',group='pan')

  

  data_fst_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pw~F[ST])')

  

  global_fst <- read.csv(paste('../../2_output/08_popGen/05_fst/10kb/',searchLG,'/global.',searchLG,'.fst',sep=''),sep='\t') %>%

    filter(CHROM==searchLG,POS > xr[1],POS<xr[2]) %>%

    select(POS,WEIR_AND_COCKERHAM_FST) %>%

    mutate(window='bolditalic(F[ST])',clr=ifelse(POS%in%searchsnp,NA,'lightgray'),

           clr2=ifelse(POS%in%searchsnp,highclr,NA))

  return(list(data_fst_pw=data_fst_pw,global_fst=global_fst,data_fst=data_fst))

}
 
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0_data/0_scripts/F3.getGxP.R

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getGxP <- function(searchLG,xr){

  np <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.pue-nig-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-pue')

  nu <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.nig-uni-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-uni')

  pu <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.pue-uni-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='pue-uni')

  

  data_pfst <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bold(-log[10] (bolditalic(p)))')

  

  npB <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.puebel-nigbel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-pue',group='bel')

  nuB <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.nigbel-unibel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-uni',group='bel')

  puB <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.puebel-unibel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='pue-uni',group='bel')

  

  npH <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.puehon-nighon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-pue',group='hon')

  nuH <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.nighon-unihon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-uni',group='hon')

  puH <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.puehon-unihon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='pue-uni',group='hon')

  

  npP <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.pueboc-nigboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-pue',group='pan') 

  nuP <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.nigboc-uniboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='nig-uni',group='pan')

  puP <- read.csv(paste('../../2_output/08_popGen/06_GxP/smoothed/10kb/',searchLG,'/gxp.pueboc-uniboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,avgp_wald) %>% mutate(run='pue-uni',group='pan')

  

  data_pfst_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bold(pw~-log[10] (bolditalic(p)))')

  



  return(list(data_pfst_pw=data_pfst_pw,data_pfst=data_pfst))

}
 
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